HPC/Applications/lammps

Binaries

As of module version lammps/2012-10-10-3 several LAMMPS binaries are provided within one module. Binaries compiled with GPU support will not run on nodes without a GPU. (CUDA libraries are deliberately only installed on GPU nodes.)

Binary name	Description
lmp_openmpi-main	The baseline binary, containing the packages shown by module help lammps.
lmp_openmpi	The distribution's default name; synonym for lmp_openmpi-main;
lmp_openmpi-gpu	The package "gpu" and all packages from main.
lmp_openmpi-user-cuda	The package "user-cuda" and all packages from main.
lmp_openmpi-jr	A custom build for user J.R.

Simply name the appropriate binary in the job file, typically as argument to mpirun:

…
mpirun  -machinefile $PBS_NODEFILE -np $PBS_NP \
    lmp_openmpi -in in.script

Benchmark

Using a sample workload from Sanket ("run9"), I tested various OpenMPI options on both node types.

LAMMPS performs best on gen2 nodes without extra options, and pretty well on gen1 nodes over ethernet(!).

Job tag	Node type	Interconnect	Additional OpenMPI options	Relative speed (1000 steps/3 hours)	Notes
gen1	gen1	IB	(none)	36
gen1srqpin	gen1	IB	-mca btl_openib_use_srq 1 -mca mpi_paffinity_alone 1	39
gen1eth	gen1	Ethernet	-mca btl self,tcp	44	fastest for gen1
gen2eth	gen2	Ethernet	-mca btl self,tcp	49
gen2srq	gen2	IB	-mca btl_openib_use_srq 1	59
gen2	gen2	IB	(none)	59	fastest for gen2

Sample job file gen1

#!/bin/bash
#PBS -l nodes=10:ppn=8:gen1
#PBS -l walltime=1:00:00:00
#PBS -N <jobname>
#PBS -A <account>
#
#PBS -o job.out
#PBS -e job.err
#PBS -m ea

# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR

mpirun  -machinefile  $PBS_NODEFILE -np $PBS_NP \
        -mca btl self,tcp \
        lmp_openmpi < lammps.in > lammps.out 2> lammps.err

Sample job file gen2

#!/bin/bash
#PBS -l nodes=10:ppn=8:gen2
#PBS -l walltime=1:00:00:00
#PBS -N <jobname>
#PBS -A <account>
#
#PBS -o job.out
#PBS -e job.err
#PBS -m ea

# change into the directory where qsub will be executed
cd $PBS_O_WORKDIR

mpirun  -machinefile  $PBS_NODEFILE -np $PBS_NP \
        lmp_openmpi < lammps.in > lammps.out 2> lammps.err

MPI/OpenMP hybrid parallel runs

LAMMPS modules since 2012 are compiled with yes-user-omp, permitting multi-threaded runs of selected pair styles, and in particular MPI/OpenMP hybrid parallel runs.

Be careful how to allocate CPU cores on compute nodes. Note the following:

• The number of cores on a node reserved for your use is determined by the qsub ppn=... parameter.
• The number of MPI tasks (call it ppn_mpi) running on a node is determined by options to mpirun.
• The number of threads that each MPI task runs with is determined by the environment variable OMP_NUM_THREADS, which is 1 by default on Carbon.
• The number of physical cores per node for gen1 and gen2 nodes is 8.
• gen2 nodes have hyperthreading active, meaning there are 16 logical cores per node. However:
  • The method shown below cannot consistenly use hyperthreading since PBS is told that nodes have exactly 8 cores. ppn requests higher than that cannot be fulfilled.
  • My (stern) own benchmarks for a memory-intensive DFT program were underwhelming.
  • The LAMMPS OpenMP author reports the same (near the end of the section):

Using threads on hyper-threading enabled cores is usually counterproductive, as the cost in additional memory bandwidth requirements is not offset by the gain in CPU utilization through hyper-threading.

Sample job script for hybrid parallel runs

In summary, the job script's essential parts are:

#!/bin/bash
#PBS -l nodes=2:ppn=8
#PBS -l walltime=1:00:00
...

ppn_mpi=2		# user choice
ppn_pbs=$( uniq -c $PBS_NODEFILE | awk '{print $1; exit}' )	# grab first (and usually only) ppn value of the job
OMP_NUM_THREADS=$(( ppn_active / ppn_mpi ))			# calculate number of threads available per MPI process (integer arithmetic!)

mpirun -x OMP_NUM_THREADS \
    -machinefile  $PBS_NODEFILE \
    --npernode $ppn_mpi \
    lmp_openmpi \
	-sf omp \
	-in in.script

Diagnostic for hybrid parallel runs

• LAMMPS echoes it parallelization scheme first thing in the output:

LAMMPS (10 Feb 2012)
  using 4 OpenMP thread(s) per MPI task
...
  1 by 2 by 2 MPI processor grid
  104 atoms
...

and near the end:

Loop time of 124.809 on 16 procs (4 MPI x 4 OpenMP) for 30000 steps with 104 atoms

• To see if OpenMP is really active, log into a compute node while a job is running and run top or psuser – The %CPU field should be about OMP_NUM_THREADS × 100%

 PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND                                                                                             
8047 stern     25   0 4017m  33m 7540 R 401.8  0.1   1:41.60 lmp_openmpi                                                                                         
8044 stern     25   0 4017m  33m 7540 R 399.9  0.1   1:43.50 lmp_openmpi                                                                                         
4822 root      34  19     0    0    0 S  2.0  0.0 115:34.98 kipmi0

References

• HPC/Submitting_Jobs/Advanced node selection#Multithreading (OpenMP)
• LAMMPS documentation for the OMP package
• Command-line options (explanation for -sf style or -suffix style)